Out of curiosity, is this a new or old world of darkness setting? I'm beginning to form an answer in my head, but I feel like there are a few more things I should know before I put it out there.
–
B.A. ThomasAug 21 '12 at 19:46

Its the new World of Darkness vanilla. I'm only using the core book.
–
CircusfreakAug 22 '12 at 19:00

The penalties I am about to list should not be specific to an individual with high or low stamina; however, the formula I am about to propose presumes a size 5 human, which contributes 5 points towards health levels in nWoD. The following suggestions also assume temperate climate (Spring in D.C.) as opposed to a drastically cold (Alaska in February) or one that is unbearably hot (July in Sahara Desert). For extreme temperatures, add one lethal if no satisfactory environmental aid can be used. This reflects the body's attempt to adjust for temperature to maintain homeostasis.

Food tracking: For every week without food fill one box in with lethal damage. In eight weeks, a character with Stamina 3 will perish. This is the standard presented in the article. Stamina 3 and 8 weeks would be the presumed upper limits of a healthy person going without food, BUT assumes that they have an adequate supply of water.

Water tracking: If you want to take it easy on them, two levels of bashing damage at the beginning of each day begun without water (as their bodies attempt to repair themselves through the night, but end up consuming vital nutrients in the process). Two additional bashing at the beginning of each day without water, convert previous day's bashing to lethal. (This isn't how the damage is normally tracked. Please be aware.)

If you want a bit more realism, 1 lethal damage for every 10 hours without water. This puts their death close to the 72 hour estimated maximum for dehydration before expiration.

(Adequate water for a 200 lb human being is about 3 liters, or about a US gallon of water (.7925 gallons) according to an online Hydration calculator (assumed maximum exercise - it's a World of Darkness game. You're probably running around.) You may want to make the ruling "one clean gallon, one good day." As a note, individuals from temperate climates also experience the ability to ignore their thirst. Anyone from dry & hot areas may need less water, or experience less wound penalties due to thirst/dehydration per their experience.)

RE-hydration should be handled more slowly. One gallon of water stops the dehydration for one day. There should be no grace period for dehydration while they are in this survival mode. Once the survival section of this game goes away, the risk of dehydration should linger for about a week or so as the body recovers and gets used to its normal water intake quotient.
(Dirty water can be worse than dehydration with parasites or diseases sapping strength and time from the character. Boiled water should count as clean water, and for added visual flavor, you may want to throw in the water turning brown as all of the parasites and other 'fun bits' die in the water ("If it's boiled and brown, drink it on down. If sat cool & clear: Live in abject fear")).

I also HIGHLY recommend watching any survival shows you can find on cable, especially Man vs Wild, 'Man Woman Wild', Dual Survival, and "SURVIVORMAN" as resource material for this type of gaming. They explore various environments and usually deal with acquiring water in every show.

Just in case it comes up, fruits are 80% water, and coconuts contain about 1/2 cup of 'water'.

Apply the wound penalties for the wound ranks as they arise as though they were through regular damage.

tldr: 1L/10hrs = without water, 1L/week = without food. Apply wound ranks. They should check to make sure food/water is edible/clean. Have fun.

You could adapt either the blood pool from Vampire or the usual damage track as an extra health track for the Characters.

Using blood pool means you can apply penalties to mental state as the people get lower and lower (except instead of going into frenzy they'll go catatonic or collapse and gain mental issues)

Using the health track means you can apply penalties to all dice pools when their food track gets too low for them.

Either one you use, treat it like a blood pool; you loose a "food" every day, eat some food to regain "food" points on your chart; when it gets low you starve, go mad, get penalties.

Using some medical data you can work out roughly how many boxes you'll need in each category (OK, Bruised, Wounded, Incap, Dead) for an average person, then add on their Stamina on top of this as extra "OK" levels.

Medical data would be a good place to start. The stages of hunger should give you a good indicator as to the effects of hunger on the human body. It should be easy to apply penalties depending on which stage you are in.